chr2-216968676-C-T

Variant names:

• chr2-216968676-C-T
• rs2244235
• ENST00000447289.1:n.511-25282C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000607591.1(TESHL):​n.114-13295C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.667 in 152,068 control chromosomes in the GnomAD database, including 34,900 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.67 (34900 hom., cov: 31)
• Consequence: TESHL ENST00000607591.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.171
• Publications: 1 publications found

Genes affected

TESHL (HGNC:52740): (testicular germ cell expressed HSF2 interacting lncRNA)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.834 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000607591.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TESHL	ENST00000447289.1	TSL:5	n.511-25282C>T		intron	N/A
	TESHL	ENST00000607591.1	TSL:3	n.114-13295C>T		intron	N/A
	TESHL	ENST00000695932.1		n.449-25282C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.667 AC: 101324 AN: 151950 Hom.: 34853 Cov.: 31

Gnomad AFR AF: 0.841

Gnomad AMI AF: 0.635

Gnomad AMR AF: 0.619

Gnomad ASJ AF: 0.653

Gnomad EAS AF: 0.756

Gnomad SAS AF: 0.553

Gnomad FIN AF: 0.581

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.588

Gnomad OTH AF: 0.663

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.667 AC: 101425 AN: 152068 Hom.: 34900 Cov.: 31 AF XY: 0.663 AC XY: 49241 AN XY: 74302

African (AFR) AF: 0.841 AC: 34907 AN: 41504

American (AMR) AF: 0.619 AC: 9462 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.653 AC: 2268 AN: 3472

East Asian (EAS) AF: 0.756 AC: 3895 AN: 5154

South Asian (SAS) AF: 0.553 AC: 2659 AN: 4812

European-Finnish (FIN) AF: 0.581 AC: 6129 AN: 10548

Middle Eastern (MID) AF: 0.646 AC: 190 AN: 294

European-Non Finnish (NFE) AF: 0.588 AC: 39937 AN: 67974

Other (OTH) AF: 0.663 AC: 1400 AN: 2112

Alfa AF: 0.625 Hom.: 39288

Bravo AF: 0.679

Asia WGS AF: 0.658 AC: 2288 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.1
DANN	Benign	0.44
PhyloP100		0.17

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2244235; hg19: chr2-217833399;